ArticleBiophysical journal2020
An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- TranslatingFrontiers in bioengineering and biotechnology · 2026Article
- Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast.Molecular biology of the cell · 2025Article
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- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 2025Article
- Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal.Nature cell biology · 2024Article
- Article
- Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.Briefings in bioinformatics · 2023Article
- Violation of the ultrastructural size principle in the dorsolateral prefrontal cortex underlies working memory impairment in the aged common marmoset (Callithrix jacchus).Frontiers in aging neuroscience · 2023Article
- Dendritic spine morphology regulates calcium-dependent synaptic weight change.The Journal of general physiology · 2022Article
- Morphological principles of neuronal mitochondria.The Journal of comparative neurology · 2022Article
- Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematicsand revealed by a three-dimensional computational framework.Proceedings. Mathematical, physical, and engineering sciences · 2021Article
- Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape.NPJ systems biology and applications · 2021Article
- Backmapping triangulated surfaces to coarse-grained membrane models.Nature communications · 2020Article
- Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations.Frontiers in physics · 2020Article
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Authors and funding
7 authors.
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Abstract
Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this work, we outline the steps for a naïve user to approach the Geometry-preserving Adaptive MeshER software version 2, a mesh generation code written in C++ designed to convert structural data sets to realistic geometric meshes while preserving the underlying shapes. We present two example cases: 1) mesh generation at the subcellular scale as informed by electron tomography and 2) meshing a protein with a structure from x-ray crystallography. We further demonstrate that the meshes generated by the Geometry-preserving Adaptive MeshER software are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.
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